Cerebral microbleeds (CMBs) can be understood as a type of target organ damage caused by hypertension. We aimed to explore the association of the CMB burden with morning blood pressure (BP) variability in patients with hypertension. We divided patients with hypertension into two groups: a group with 1–10 CMBs and a group with more than 10 CMBs. The duration, grade, medication, and control of hypertension were recorded in all patients. Morning home BP measurements were performed every 3 days for a month. A total of 791 patients were recruited. Full factor model analysis showed that higher morning home diastolic BP variability (standard deviation [SD], OR = 1.080, 95% CI: 1.024–1.140, P = .005; coefficient of variation [CV], OR = 1.076, 95% CI: 1.028–1.128, P = .002) was associated with more than 10 CMBs. Morning home systolic and diastolic blood pressure variability (SD, CV, average real variability) in more than 10 non‐lobar CMBs group was significantly higher than that in 1–10 non‐lobar CMBs group (P < .05).The multivariate analysis showed higher morning home diastolic blood pressure variability (SD, OR = 1.124, 95% CI: 1.031–1.224, P = .008; CV, OR = 1.099, 95% CI: 1.019–1.186, P = .015; average real variability, OR = 1.055, 95% CI: 0.995–1.120, P = .075) was associated with more than 10 non‐lobar CMBs. There was no significant relationship between morning home systolic blood pressure variability and more than 10 non‐lobar CMBs (P > .05). Higher morning home diastolic blood pressure variability was associated with more than 10 CMBs and more than 10 non‐lobar CMBs.